Pig genome annotation: A Gene Wish List

A Wish List of Genes for Annotation (version 3.26)

(Matches to BACs by their Genome Locations Based on Pig Genome Build v.9 (Data Downloads as of Mar. 7, 2010 )

Info:

Purpose: Help users to find where to go from gene names to their genome locations/BACs in order to locate a starting spot in the pig genome to bring into Otterlace for annotations.
Methods: The gene locations are determined in 2 ways: Ensembl predictions and Blasts. Clones are sought based on their overlapping genome locations with that of your gene.
Terms: Finished BACs: A total of 811 "finished" clones that met the "golden standard" of finished sequencing quality. Unfinished clones: Out of 15,837 clones on the "unfinished clones" list, only 1,769 have been processed to have genome locations. FPC clones: 254K+ of those clones in the sequencing pipeline
Related links:

HINTS:

Owner/Status info: : Someone has this gene on their wish-list to annotate. : This gene is to be annotated. : This gene has been annotated (click to check for details - maybe only a gene variant is annotated. The ultimate annotator list is from Otterlace entries; This list only provides a working reference).
Additional info: : have orthologous gene information. : have refseq information. : details (click for more)
Ensembl Gene ID, Genome Locations, and BAC names are all hyper-linked to Ensembl database

( Go to genes whose symbol start with: 1, 5, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z )
Search results:	Show Finished BAC Show unFinished BAC

User Gene List			Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)
Symbol	Owner/ Status	Ensembl Gene ID	Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)

MIS		ENSSSCG00000000271	5:17125841-17131706
MIS		location ⇒	2:47139160-47137716		CU929035,CH242-88G19,2:47137529-47139881 (Clone quality: bE88G19 on chr=2; Num_of_Contigs=27; )
MIST		ENSSSCG00000007600	3:4619434-4619988		CU855506,CH242-234E8,3:4575665-4638358 (Clone quality: bE234E8 on chr=3; Num_of_Contigs=6; )
MITD1		ENSSSCG00000008185	3:50772783-50788131		FP102935,CH242-65E14,3:50772545-50793979 (Clone quality: bE65E14 on chr=3; Num_of_Contigs=4; )
MITF		ENSSSCG00000011512	13:43319564-43335697		CU896681,CH242-472G6,13:43319068-43336184 (Clone quality: bE472G6 on chr=13; Num_of_Contigs=16; )
MJD6		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
MKI67IP		ENSSSCG00000015730	15:28177109-28181717
MKKS		ENSSSCG00000007064	17:19319595-19329289		CU914520,CH242-71M21,17:19305409-19334343 (Clone quality: bE71M21 on chr=17; Num_of_Contigs=7; )
MKL1		ENSSSCG00000000075	5:4225678-4243378
MKL2		ENSSSCG00000007880	3:26509056-26509685
MKL2		location ⇒	3:26440392-26440444		CU896561,CH242-61G18,3:26434529-26443926 (Clone quality: bE61G18 on chr=3; Num_of_Contigs=16; )
MKL2		location ⇒	3:26463039-26463143		CU896561,CH242-61G18,3:26462292-26465050 (Clone quality: bE61G18 on chr=3; Num_of_Contigs=16; )
MKL2		location ⇒	3:26464248-26464544		CU896561,CH242-61G18,3:26462292-26465050 (Clone quality: bE61G18 on chr=3; Num_of_Contigs=16; )
MKL2		location ⇒	3:26464602-26465043		CU896561,CH242-61G18,3:26462292-26465050 (Clone quality: bE61G18 on chr=3; Num_of_Contigs=16; )
MKLN1		ENSSSCG00000016549	18:15657789-15820766
MKNK1		ENSSSCG00000003898	6:117942956-118002452
MKNK2		ENSSSCG00000013448	2:46984136-47152503
MKNK2		location ⇒	2:46984326-46984425		FP236669,CH242-487E14,2:46980700-46987371 (Clone quality: bE487E14 on chr=2; Num_of_Contigs=9; )
MKNK2		location ⇒	2:46987279-46987353		FP236669,CH242-487E14,2:46980700-46987371 (Clone quality: bE487E14 on chr=2; Num_of_Contigs=9; )
MKNK2		location ⇒	2:47146856-47146945		CU929035,CH242-88G19,2:47144008-47152805 (Clone quality: bE88G19 on chr=2; Num_of_Contigs=27; )
MKNK2		location ⇒	2:47147046-47147145		CU929035,CH242-88G19,2:47144008-47152805 (Clone quality: bE88G19 on chr=2; Num_of_Contigs=27; )
MKRN1		ENSSSCG00000016498	18:7737573-7761669
MKRN3		ENSSSCG00000004836	1:149905497-149906960		CU074319,CH242-122F20,1:149857660-149957090 (Clone quality: bE122F20 on chr=1; Num_of_Contigs=2; )
MKS1		ENSSSCG00000017635	12:32484485-32497355		CU571372,CH242-73D9,12:32463161-32524857 (Clone quality: bE73D9 on chr=12; Num_of_Contigs=4; )
MLANA		ENSSSCG00000005206	1:226137877-226150391		CU694831,CH242-171I5,1:226079471-226214054 (Clone quality: bE171I5 on chr=1; Num_of_Contigs=2; )
MLC		ENSSSCG00000000389	5:20614713-20617851		CU498845,CH242-111P13,5:20599927-20631966 (Clone quality: bE111P13 on chr=5; Num_of_Contigs=18; )
MLC		ENSSSCG00000000978	5:99947301-99966330
MLC		ENSSSCG00000016752	18:49568947-49571355		CU928907,CH242-155A21,18:49534481-49598883 (Clone quality: bE155A21 on chr=18; Num_of_Contigs=2; )
MLC		ENSSSCG00000000381	5:20477435-20480574		CU694915,CH242-453C18,5:20460687-20504457 (Clone quality: bE453C18 on chr=5; Num_of_Contigs=10; )
MLC		location ⇒	5:99958354-99958238
MLC		location ⇒	5:99962382-99962259
MLC		location ⇒	5:99964820-99964663
MLC		location ⇒	5:99966330-99966111
MLC1		ENSSSCG00000000978	5:99947301-99966330
MLEC		ENSSSCG00000009914	14:40665604-40675468		CU062553,CH242-319N22,14:40664399-40687679 (Clone quality: bE319N22 on chr=14; Num_of_Contigs=5; )
MLF1		ENSSSCG00000015785	15:42999826-43027571
MLF1IP		ENSSSCG00000015785	15:42999826-43027571
MLF2		ENSSSCG00000000690	5:59987904-59993368		CU457492,CH242-370K21,5:59980691-59995678 (Clone quality: bE370K21 on chr=5; Num_of_Contigs=10; )
MLH1		location ⇒	13:18165304-18165404		CU856332,CH242-416J21,13:18162157-18172638 (Clone quality: bE416J21 on chr=13; Num_of_Contigs=14; )
MLH1		location ⇒	13:18173193-18173081		CU856332,CH242-416J21,13:18172739-18182151 (Clone quality: bE416J21 on chr=13; Num_of_Contigs=14; )
MLH1		location ⇒	13:18175520-18175432		CU856332,CH242-416J21,13:18172739-18182151 (Clone quality: bE416J21 on chr=13; Num_of_Contigs=14; )
MLH1		location ⇒	13:18177224-18177129		CU856332,CH242-416J21,13:18172739-18182151 (Clone quality: bE416J21 on chr=13; Num_of_Contigs=14; )
MLH3		ENSSSCG00000002378	7:106474202-106499219	CT737372,CH242-134B18,7:106458379-106624048 (Clone quality: bE134B18 on chr=7; Num_of_Contigs=4; )
MLKL		ENSSSCG00000002716	6:9416569-9499014
MLL		ENSSSCG00000013508	2:48584668-48614909		CU972396,CH242-401E10,2:48541506-48658119 (Clone quality: bE401E10 on chr=2; Num_of_Contigs=4; )
MLL		ENSSSCG00000004761	1:137007636-137013523		CU633257,CH242-257P7,1:137003112-137140964 (Clone quality: bE257P7 on chr=1; Num_of_Contigs=3; )
MLL2		ENSSSCG00000000191	5:13861859-13872472		CU633656,CH242-19B12,5:13845430-13882549 (Clone quality: bE19B12 on chr=5; Num_of_Contigs=10; )
MLL2		location ⇒	5:13677863-13677680		CU928246,CH242-133O18,5:13649873-13683519 (Clone quality: bE133O18 on chr=5; Num_of_Contigs=7; )
MLL2		location ⇒	5:13681772-13681625		CU928246,CH242-133O18,5:13649873-13683519 (Clone quality: bE133O18 on chr=5; Num_of_Contigs=7; )
MLL2		location ⇒	5:13863298-13863115		CU633656,CH242-19B12,5:13845430-13882549 (Clone quality: bE19B12 on chr=5; Num_of_Contigs=10; )

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 601-650, 651-700, 701-750, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-46

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$version: 3.26; Updates: Mar. 6, 2010; Apr. 20, 2010; Aug 21, 2010

Related publications:

Martien Groenen, Alan Archibald, Hirohide Uenishi, Christopher Tuggle, Yasuhiro Takeuchi, Max Rothschild, Claire Rogel-Gaillard, ... Denis Milan, Hendrik-Jan Megens, ... Zhi-Liang Hu, Sean J. Humphray, ... James M. Reecy, ..., Gary A. Rohrer, ... Shuhong Zhao, Jane Rogers, Carol Churcher & Lawrence B. Schook. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398 (15 November 2012).